RetrogeneDB ID: retro_pabe_1002

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:50137738..50140087(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CTAGE5
• Ensembl ID: ENSPPYG00000005768
• Aliases: None
• Description: CTAGE family, member 5 [Source:HGNC Symbol;Acc:7057]

Sequence

>retro_pabe_1002
AGGGTTGTGGCAGCACTGCCTGAAGGCAGGAGACCAGATTCGAATCCTTATGGATTTCCATGGGAATTGGTGATATGTGC
AGCTGTCCTGGGATTTGTTGCTGTTCCCTTTTTCTTGTGGAGAAGTTTTAGATCGGTTAGGAGTCGGCTTTATGTGGGAA
GAGAGAAAGAGCTTGCTGTAGAGCTTTCTGGACTAATTGAAGAAAAATGTAGACTACTTGAAAAATTTAGCCTTGTTCAA
AAAGAGTATGAAGGCTATGAAGTAGAGTCATCTTTAGAGGATGCCAGCTTTGAGAAGGAGGCAACAGAAGCACAAAGTTT
GGAGGCAACCTGTGAAAAGCTGAACAGGTCCAATTCTGAACTGGAGCATGAAATACTCTGTCTAGAAAAGGAGTTAAAAG
AAGAGAAATCTAAACATTCTGAACAAGATAAGGTGATGGCGGATATTTCCAAAAGGATACAGTCTCTAGAAGATGAGTCA
AAATCCCTCAAATCCCAAGTAGCTGAAGCCAAAATGACCTGGAAGAGATTTCAAATGAATGAAGAACAAATGAAGATAAG
AATACAAGACGCTTTGAATGAAAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGCAGTATGGAAAG
AACAAGTGAGTGAACTTAATAAACAGAAAATAACATTTGAAAACTCCAAAGTACATGCAGAACAAGTTCTAAATGATAAA
GAAAAGCACATCGAGACTCTGACTGAACGCCTGCTAAAGATCAAAGATCAGGCTGCTATGCTGGAAGGAGACATAACGGA
TGATGGTAACTTGGAATTAGAAATGAACAGTGAATCGGAAGATGGTGCTTACTTAGATAATCCTCCAAAAGGAACTTTGA
AGAAACTGATTCATGCTGCTAAGTTAAATGCTTCTTTAACAACCTTAGAAGGAGAAAGAAACCAAATTTATATTCAGTTA
TCTGAAGTTGATAAAACCAAGGAAGAGCTTAGAGAGCATATTAAAAATCTTCAGATGGAACAAGCATCTTTGCAGTCAGA
AAACACACATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAGGTAATGACAGAATTATATCAAGAAAATAAAA
TGAAGCTCTACAGGAAATTAATAGTAGAGGAAAATAACCGGCTAGAGAAAGAGAAACTTTCTAAAGTAGACGAAATGATC
AGCCATGCCACTGAAGAGCTGGAGACCTGCAGAGAGCGAGCCAAAGAACTTGAAGAAGAATTTGAGAGAACTATTCATTT
TTATCAAGGGAAGATTATTTCCCATGAGAAAAAAGCACACGATAATTGTTTGGCAGCACAGACTGCTGAAAGAAACCTCA
ATGATTTAAGGAAAGAAAATGCTCACAACAGACAAAAATTAGCTGAAACAGCGTTTAAAATTAAACTTTTAGAAAAAGAT
CCTTATGCACTTGATGTTCCAAATACAGCGTTTGGCAGAGAGCATTCCTCATATGGTCCCTCACCATTGGGTCGGCCTTC
ATCTGAAACGAGAGCTTTTCTCTATCCTCCAACTTTGTTGGAGGGTCCACTCAGACTCTCACCTCTGCTTCCAGCGGGAG
GAGGAAGAGGCCCAAGAGGCCCAGGGAATCCTCGGGACCACCACATTACCAAGGAAAGAGGAGAATCAACCTGTGATAGG
TTTACCGATCCTCACAAGGCTCCTTCTGACACTGGGCCCCTGCCACCTCCGTGGGAACAGGACTGTAGGATGATGTTTCC
TCCACCAGGACGATCATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAATTGTGCTAGACATG
CTGGGCCAGCAGAACTCAGAAGTTTTAATATACCTTCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCC
AGTAGAAATGATACCAAAGATAATCTTGGTAATTTAAATGTGCCTGATTCATCTCTCCCCGCCGACAGTGAAGGAACTGG
TCCTGGTTTTGTTCCTCCACCTCTTGCTCGAATCAGAAGTCCATTGTTTCCAGTGGATATGAGGGGCCCGTTCATGAGAA
GAGGACCTCGTTTCGCTCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCCAGATTATTTTCCACCAAGGGATTTTCCA
GGTCCACCACGTGCTCCATTTGCAATGAGAAATGTCTATCCACCGAAGGGTTTTCCTCCTTACCTTCCCCCGAGACCTGG
ATTCCCCCCTGACACTCCCACATTCTGAAGGTAGAGTGAGTTGCCTTCATGGTTAAGTCTGCCTTCAAATGAGCCTGCTA
CTGAAGATCCAGAACCACAGCAAGAAACC

Alignment

ORF - retro_pabe_1002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.21 %
• Parental protein coverage: 58.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVVAALPEGMRPDSNPYGFPWELVICAAVVGFFAVLFFSWRSFRSVSNQCYTKRIPVFSEKQTLLLENKI
          RVVAALPEG.RPDSNPYGFPWELVICAAV.GF.AV.FF.WRSFRSV....Y..R..........L.E.K.
Retrocopy RVVAALPEGRRPDSNPYGFPWELVICAAVLGFVAVPFFLWRSFRSVRSRLYVGREKELAVELSGLIEEKC

Parental  RRVFTCDVALFQYEGYEVESSLKNASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHS
          R...........YEGYEVESSL..ASFEKEATEAQSLEATCEKLNRSNSELE.EILCLEKELKEEKSKHS
Retrocopy RLLEKFSLVQKEYEGYEVESSLEDASFEKEATEAQSLEATCEKLNRSNSELEHEILCLEKELKEEKSKHS

Parental  EQDELMADISKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSELQESQKQLLQDAE
          EQD..MADISKRIQSLEDESKSLKSQVAEAKMT.K.FQMNEE..KI.I.DALNENS.LQESQKQLLQ.A.
Retrocopy EQDKVMADISKRIQSLEDESKSLKSQVAEAKMTWKRFQMNEEQMKIRIQDALNENSQLQESQKQLLQEAA

Parental  VWKEQVSELNKQKVTFEDSKVHAEQVLNDKENHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESE
          VWKEQVSELNKQK.TFE.SKVHAEQVLNDKE.HI.TLTERLLK.KD.AAML..DITDD.NLELEMNSESE
Retrocopy VWKEQVSELNKQKITFENSKVHAEQVLNDKEKHIETLTERLLKIKDQAAMLEGDITDDGNLELEMNSESE

Parental  NGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTH
          .GAYLDNPPKG.LKKLIHAAKLNASL.TLEGERNQIYIQLSEVDKTKEEL.EHIKNLQ.EQASLQSENTH
Retrocopy DGAYLDNPPKGTLKKLIHAAKLNASLTTLEGERNQIYIQLSEVDKTKEELREHIKNLQMEQASLQSENTH

Parental  FENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEE
          FE.ENQKLQQKLKVMTELYQEN.MKL.RKL.VEEN.RLEKE.KLSKVDE.ISHATEELET.R.RAK.LEE
Retrocopy FESENQKLQQKLKVMTELYQENKMKLYRKLIVEENNRLEKE-KLSKVDEMISHATEELETCRERAKELEE

Parental  ELERTIHSYQGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNT
          E.ERTIH.YQG.IISHEKKAHDN.LAA..AERNLNDLRKENAHNRQKL.ET..K..LLEKDPYALDVPNT
Retrocopy EFERTIHFYQGKIISHEKKAHDNCLAAQTAERNLNDLRKENAHNRQKLAETAFKIKLLEKDPYALDVPNT

Parental  AFGREHSPYGPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCD
          AFGREHS.YGPSPLG.PSSETRAFL.PPTLLEGPLRLSPLLP.GGGRG.RGPGNP.DH.IT.ERGES.CD
Retrocopy AFGREHSSYGPSPLGRPSSETRAFLYPPTLLEGPLRLSPLLPAGGGRGPRGPGNPRDHHITKERGESTCD

Parental  RLTNPHRAPSDTGSLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDK
          R.T.PH.APSDTG.L.PPWEQD.RMMFPPPG.SYPDSALPPQRQDRF.SN..R..GPAELRSFN.PSLDK
Retrocopy RFTDPHKAPSDTGPLPPPWEQDCRMMFPPPGRSYPDSALPPQRQDRFYSNCARHAGPAELRSFNIPSLDK

Parental  MDGSMPSEMESSRNDTKDDLGNLNVPDSSLPTENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFP
          MDGSMPSEMESSRNDTKD.LGNLNVPDSSLP...E.TGPGFVPPPLA.IR.PLFPVD.RGPF.RRGP.F.
Retrocopy MDGSMPSEMESSRNDTKDNLGNLNVPDSSLPADSEGTGPGFVPPPLARIRSPLFPVDMRGPFMRRGPRFA

Parental  PPPPGAVFGASRDYFPPRDFPGPPHAPFAMRNVYPPRGFPPYLPPRPGFFPPP-PHSEGR-SEFPSGLIP
          PPPPG..FGAS.DYFPPRDFPGPP.APFAMRNVYPP.GFPPYLPPRPGF.P...PHSEGR.SE.PS.L..
Retrocopy PPPPGTMFGASPDYFPPRDFPGPPRAPFAMRNVYPPKGFPPYLPPRPGFPPDT>PHSEGR<SELPSWLSL

Parental  PSNEPATEHPEPQQET
          PSNEPATE.PEPQQET
Retrocopy PSNEPATEDPEPQQET

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.20 RPM
SRP007412_cerebellum	0.00 RPM	8.88 RPM
SRP007412_heart	0.00 RPM	9.60 RPM
SRP007412_kidney	0.00 RPM	44.81 RPM
SRP007412_liver	0.00 RPM	43.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1002 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1002 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002 , retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286, retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95,